merging changes with ChIP-seq and RNA-seq pipelinesMerge branch 'acti…

…veDev' of https://github.com/CCBR/Pipeliner into activeDev

Results-template/Scripts/pcacall.R

@@ -2,13 +2,14 @@
 ## grab args
 args <- commandArgs(trailingOnly = TRUE)
 DIR <- args[1]
+outHtml <- args[2]
 # Sys.setenv(RSTUDIO_PANDOC="/Applications/RStudio.app/Contents/MacOS/pandoc")
 setwd(DIR) # new 
-rmarkdown::render("PcaReport.Rmd", params = list(
+rmarkdown::render("PcaReport.Rmd",output_file=outHtml, params = list(
     folder = args[1],
-    sampleinfo = args[2],
-    data = args[3],
-    projectId = args[4],
-    projectDesc = args[5]
+    sampleinfo = args[3],
+    data = args[4],
+    projectId = args[5],
+    projectDesc = args[6]
   ))
 

gui/frame.py

@@ -352,7 +352,17 @@ def init_work_dir( self ):
             showinfo( "Success", "The work directory has successfully initialized!")
         else :
             showerror( "Symlink failed", "" )
-
+
+    def popup_warning(self, filename):
+        try:
+            fname = self.workpath.get() + '/' + filename
+            fh = open(fname, 'r')
+            return False
+        except IOError:
+            print("Could not find required file {} in your working directory:{}".format(filename, self.workpath.get()))
+            showerror("Error","{0} file not found!\nDid you initialize the working directory?\nDid you copy {0} into the working directory?".format(filename))
+            return True
+
     def popup_window( self, text, filename ) :
         top = Toplevel()
 
@@ -697,6 +707,11 @@ def readpaste( self, ftype, comments ):
         return
 
     def dryrun( self ) :
+        pl = self.pipeline_name
+        print("Drying-running: {}".format(pl))
+        if pl == 'RNAseq':
+            if self.popup_warning('groups.tab') or self.popup_warning('contrasts.tab'):
+                return
         self.makejson("none")
         #self.run_button.config( state='active' )
         return self.cmd( "--dryrun -p -s %s/Snakefile --rerun-incomplete -d %s" % ( self.workpath.get(), self.workpath.get()))